Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world. Here, we describe some of the ways we have been able to realize this through the use of parallelization on all levels, combined with a constant focus on absolute performance. Release 4.6 of GROMACS uses SIMD acceleration on a wide range of architectures, GPU offloading acceleration, and both OpenMP and MPI parallelism within and between nodes, respectively. The recent work on acceleration made it necessary to revisit the fundamental algorithms of molecular simulation, including the concept of neighborsearching, and we discuss the present and future challenges we see for exascale simulation - in particular a very fine-grained task parallelism. We also discuss the software management, code peer review and continuous integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin

Observation of enhanced rate coefficients in the H2+_2^+ + H2_2 →\rightarrow H3+_3^+ + H reaction at low collision energies

The energy dependence of the rate coefficient of the H$_2^+\ + {\rm H}_2 \rightarrow {\rm H}_3^+ + {\rm H}$ reaction has been measured in the range of collision energies between $k_\mathrm{B}\cdot 10$ K and $k_\mathrm{B}\cdot 300$ mK. A clear deviation of the rate coefficient from the value expected on the basis of the classical Langevin-capture behavior has been observed at collision energies below $k_\mathrm{B}\cdot 1$ K, which is attributed to the joint effects of the ion-quadrupole and Coriolis interactions in collisions involving ortho-H$_2$ molecules in the $j = 1$ rotational level, which make up 75% of the population of the neutral H$_2$ molecules in the experiments. The experimental results are compared to very recent predictions by Dashevskaya, Litvin, Nikitin and Troe (J. Chem. Phys., in press), with which they are in agreement.Comment: 14 pages, 3 figure

Optically pumped 1.3 μm room-temperature InAs quantum-dot micro-disk lasers directly grown on (001) silicon

Direct integration of high-performance laser diodes on silicon will dramatically transform the world of photonics, expediting the progress toward low-cost and compact photonic integrated circuits (PICs) on the mainstream silicon platform. Here, we report, to the best of our knowledge, the first 1.3 μm room-temperature continuous-wave InAs quantum-dot micro-disk lasers epitaxially grown on industrial-compatible Si (001) substrates without offcut. The lasing threshold is as low as hundreds of microwatts, similar to the thresholds of identical lasers grown on a GaAs substrate. The heteroepitaxial structure employed here does not require the use of an absorptive germanium buffer and/or dislocation filter layers, both of which impede the efficient coupling of light from the laser active regions to silicon waveguides. This allows for full compatibility with the extensive silicon-on-insulator (SOI) technology. The large-area virtual GaAs (on Si) substrates can be directly adopted in various mature in-plane laser configurations, both optically and electrically. Thus, this demonstration represents a major advancement toward the commercial success of fully integrated silicon photonics

1.3-μm InAs quantum-dot micro-disk lasers on V-groove patterned and unpatterned (001) silicon

We report comparison of lasing dynamics in InAs quantum dot (QD) micro-disk lasers (MDLs) monolithically grown on V-groove patterned and planar Si (001) substrates. TEM characterizations reveal abrupt interfaces and reduced threading dislocations in the QD active regions when using the GaAs-on-V-grooved-Si template. The improved crystalline quality translates into lower threshold power in the optically pumped continuous-wave MDLs. Concurrent evaluations were also made with devices fabricated simultaneously on lattice-matched GaAs substrates. Lasing behaviors from 10 K up to room temperature have been studied systematically. The analyses spotlight insights into the optimal epitaxial scheme to achieve low-threshold lasing in telecommunication wavelengths on exact Si (001) substrates

Growth hormone response to growth hormone-releasing peptide-2 in growth hormone-deficient Little mice

OBJECTIVE: To investigate a possible direct, growth hormone-releasing, hormone-independent action of a growth hormone secretagogue, GHRP-2, in pituitary somatotroph cells in the presence of inactive growth hormonereleasing hormone receptors. MATERIALS AND METHODS: The responses of serum growth hormone to acutely injected growth hormone-releasing P-2 in lit/litmice, which represent a model of GH deficiency arising frommutated growth hormone-releasing hormonereceptors, were compared to those observed in the heterozygous (lit/&#43;) littermates and wild-type (&#43;/&#43;) C57BL/6J mice. RESULTS: After the administration of 10 mcg of growth hormone-releasing P-2 to lit/lit mice, a growth hormone release of 9.3±1.5 ng/ml was observed compared with 1.04±1.15 ng/ml in controls (p<0.001). In comparison, an intermediate growth hormone release of 34.5±9.7 ng/ml and a higher growth hormone release of 163±46 ng/ml were induced in the lit/&#43; mice and wild-type mice, respectively. Thus, GHRP-2 stimulated growth hormone in the lit/lit mice, and the release of growth hormone in vivo may be only partially dependent on growth hormone-releasing hormone. Additionally, the plasma leptin and ghrelin levels were evaluated in the lit/lit mice under basal and stimulated conditions. CONCLUSIONS: Here, we have demonstrated that lit/lit mice, which harbor a germline mutation in the Growth hormone-releasing hormone gene, maintain a limited but statistically significant growth hormone elevation after exogenous stimulation with GHRP-2. The present data probably reflect a direct, growth hormone-independent effect on Growth hormone S (ghrelin) stimulation in the remaining pituitary somatotrophs of little mice that is mediated by growth hormone S-R 1a

Supporting antidepressant discontinuation: the development and optimisation of a digital intervention for patients in UK primary care using a theory, evidence and person-based approach.

OBJECTIVES: We aimed to develop a digital intervention to support antidepressant discontinuation in UK primary care that is scalable, accessible, safe and feasible. In this paper, we describe the development using a theory, evidence and person-based approach. DESIGN: Intervention development using a theory, evidence and person-based approach. SETTING: Primary Care in the South of England. PARTICIPANTS: Fifteen participants with a range of antidepressant experience took part in 'think aloud' interviews for intervention optimisation. INTERVENTION: Our digital intervention prototype (called 'ADvisor') was developed on the basis of a planning phase consisting of qualitative and quantitative reviews, an in-depth qualitative study, the development of guiding principles and a theory-based behavioural analysis. Our optimisation phase consisted of 'think aloud' interviews where the intervention was iteratively refined. RESULTS: The qualitative systematic review and in-depth qualitative study highlighted the centrality of fear of depression relapse as a key barrier to discontinuation. The quantitative systematic review showed that psychologically informed approaches such as cognitive-behavioural therapy were associated with greater rates of discontinuation than simple advice to reduce. Following a behavioural diagnosis based on the behaviour change wheel, social cognitive theory provided a theoretical basis for the intervention. The intervention was optimised on the basis of think aloud interviews, where participants suggested they like the flexibility of the system and found it reassuring. Changes were made to the tone of the material and the structure was adjusted based on this qualitative feedback. CONCLUSIONS: 'ADvisor' is a theory, evidence and person-based digital intervention designed to support antidepressant discontinuation. The intervention was perceived as helpful and reassuring in optimisation interviews. Trials are now needed to determine the feasibility, clinical and cost-effectiveness of this approach

Simulations of electromagnetic effects in high frequency capacitively coupled discharges using the Darwin approximation

The Darwin approximation is investigated for its possible use in simulation of electromagnetic effects in large size, high frequency capacitively coupled discharges. The approximation is utilized within the framework of two different fluid models which are applied to typical cases showing pronounced standing wave and skin effects. With the first model it is demonstrated that Darwin approximation is valid for treatment of such effects in the range of parameters under consideration. The second approach, a reduced nonlinear Darwin approximation-based model, shows that the electromagnetic phenomena persist in a more realistic setting. The Darwin approximation offers a simple and efficient way of carrying out electromagnetic simulations as it removes the Courant condition plaguing explicit electromagnetic algorithms and can be implemented as a straightforward modification of electrostatic algorithms. The algorithm described here avoids iterative schemes needed for the divergence cleaning and represents a fast and efficient solver, which can be used in fluid and kinetic models for self-consistent description of technical plasmas exhibiting certain electromagnetic activity

Raman scattering from fractals. Simulation on large structures by the method of moments

We have employed the method of spectral moments to study the density of vibrational states and the Raman coupling coefficient of large 2- and 3- dimensional percolators at threshold and at higher concentration. We first discuss the over-and under-flow problems of the procedure which arise when -like in the present case- it is necessary to calculate a few thousand moments. Then we report on the numerical results; these show that different scattering mechanisms, all {\it a priori} equally probable in real systems, produce largely different coupling coefficients with different frequency dependence. Our results are compared with existing scaling theories of Raman scattering. The situation that emerges is complex; on the one hand, there is indication that the existing theory is not satisfactory; on the other hand, the simulations above threshold show that in this case the coupling coefficients have very little resemblance, if any, with the same quantities at threshold.Comment: 26 pages, RevTex, 8 figures available on reques

Magnetic Field Draping in Induced Magnetospheres: Evidence from the MAVEN Mission to Mars

The Mars Atmosphere and Volatile EvolutioN (MAVEN) mission has been orbiting Mars since 2014 and now has over 10,000 orbits which we use to characterize Mars' dynamic space environment. Through global field line tracing with MAVEN magnetic field data we find an altitude dependent draping morphology that differs from expectations of induced magnetospheres in the vertical ($\hat Z$ Mars Sun-state, MSO) direction. We quantify this difference from the classical picture of induced magnetospheres with a Bayesian multiple linear regression model to predict the draped field as a function of the upstream interplanetary magnetic field (IMF), remanent crustal fields, and a previously underestimated induced effect. From our model we conclude that unexpected twists in high altitude dayside draping ($>$800 km) are a result of the IMF component in the $\pm \hat X$ MSO direction. We propose that this is a natural outcome of current theories of induced magnetospheres but has been underestimated due to approximations of the IMF as solely $\pm \hat Y$ directed. We additionally estimate that distortions in low altitude ($<$800 km) dayside draping along $\hat Z$ are directly related to remanent crustal fields. We show dayside draping traces down tail and previously reported inner magnetotail twists are likely caused by the crustal field of Mars, while the outer tail morphology is governed by an induced response to the IMF direction. We conclude with an updated understanding of induced magnetospheres which details dayside draping for multiple directions of the incoming IMF and discuss the repercussions of this draping for magnetotail morphology.Comment: Accepted in Journal of Geophysical Research: Space Physic

New approaches to ultrasensitive magnetic resonance

Spectroscopic methods tend to exhibit an inverse correlation between sensitivity and the ability to discriminate between similar structures. Were they obtainable with adequate sensitivity, magnetic resonance spectra could resolve structural controversies involving the nature of clusters, ions, semiconductor defects and catalytic intermediates. This paper describes several novel approaches to magnetic resonance, which have in common that the spins are coupled to other degrees of freedom in order to obtain nonequilibrium polarization and/or greater detection sensitivity. The methods under development include single-ion electron spin resonance (ESR) detected by ion trapping frequencies, catalyst NMR detected by the branching ratio to different spin symmetry species, and semiconductor nuclear magnetic resonance (NMR) detected via the circular polarization of luminescence